Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: J3GN9

Calculation Name: 2V0X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V0X

Chain ID: A

ChEMBL ID:

UniProt ID: Q61033

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1757116.292369
FMO2-HF: Nuclear repulsion 1681613.429442
FMO2-HF: Total energy -75502.862927
FMO2-MP2: Total energy -75719.499723


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:465:HIS)


Summations of interaction energy for fragment #1(A:465:HIS)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-4.381-1.0470.19-1.331-2.1930.008
Interaction energy analysis for fragmet #1(A:465:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.028
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A467LEU0-0.059-0.0133.595-4.090-1.2860.065-1.174-1.6950.008
4A468THR0-0.011-0.0195.3760.4430.485-0.001-0.005-0.0360.000
5A469THR0-0.015-0.0488.931-0.117-0.1170.0000.0000.0000.000
6A470LEU0-0.033-0.01112.5220.0410.0410.0000.0000.0000.000
7A471GLY0-0.0130.00515.768-0.016-0.0160.0000.0000.0000.000
8A472VAL00.0130.00215.9580.0270.0270.0000.0000.0000.000
9A473GLU-1-0.975-0.97111.071-0.028-0.0280.0000.0000.0000.000
10A489PRO0-0.022-0.01631.379-0.005-0.0050.0000.0000.0000.000
11A490SER0-0.012-0.01029.9700.0140.0140.0000.0000.0000.000
12A491PHE00.0220.01024.643-0.019-0.0190.0000.0000.0000.000
13A492PRO0-0.010-0.00126.6970.0170.0170.0000.0000.0000.000
14A493LEU0-0.004-0.00327.859-0.006-0.0060.0000.0000.0000.000
15A494HIS00.0830.03521.2480.0120.0120.0000.0000.0000.000
16A495GLU-1-0.857-0.93926.042-0.148-0.1480.0000.0000.0000.000
17A496SER00.008-0.00924.2900.0090.0090.0000.0000.0000.000
18A497ILE0-0.0130.00426.5010.0160.0160.0000.0000.0000.000
19A498LEU0-0.0020.00428.7780.0150.0150.0000.0000.0000.000
20A499LYS10.8740.94329.2130.0890.0890.0000.0000.0000.000
21A500VAL00.0290.02028.5970.0110.0110.0000.0000.0000.000
22A501VAL00.004-0.00831.4410.0100.0100.0000.0000.0000.000
23A502GLU-1-0.907-0.94234.390-0.078-0.0780.0000.0000.0000.000
24A503GLU-1-0.841-0.91831.905-0.049-0.0490.0000.0000.0000.000
25A504GLU-1-0.808-0.89234.958-0.024-0.0240.0000.0000.0000.000
26A505TRP0-0.069-0.05437.4320.0020.0020.0000.0000.0000.000
27A506GLN0-0.068-0.02938.4270.0030.0030.0000.0000.0000.000
28A507GLN0-0.073-0.05241.0790.0010.0010.0000.0000.0000.000
29A508ILE00.0090.02042.3470.0010.0010.0000.0000.0000.000
30A509ASP-1-0.853-0.89843.792-0.014-0.0140.0000.0000.0000.000
31A510ARG10.8120.90837.1840.0320.0320.0000.0000.0000.000
32A511GLN0-0.036-0.02742.1040.0000.0000.0000.0000.0000.000
33A512LEU00.0080.02239.048-0.003-0.0030.0000.0000.0000.000
34A513PRO00.0110.00334.5410.0050.0050.0000.0000.0000.000
35A514SER00.0210.01736.0160.0000.0000.0000.0000.0000.000
36A515VAL00.0640.02431.7370.0010.0010.0000.0000.0000.000
37A516ALA0-0.028-0.01831.9120.0040.0040.0000.0000.0000.000
38A517CYS0-0.040-0.03131.0850.0030.0030.0000.0000.0000.000
39A518ARG10.9660.99426.951-0.033-0.0330.0000.0000.0000.000
40A519TYR0-0.012-0.02125.1890.0060.0060.0000.0000.0000.000
41A520PRO00.0160.02628.782-0.006-0.0060.0000.0000.0000.000
42A521VAL00.0470.03631.4810.0000.0000.0000.0000.0000.000
43A522SER0-0.005-0.00431.3670.0060.0060.0000.0000.0000.000
44A523SER00.000-0.00833.785-0.002-0.0020.0000.0000.0000.000
45A524ILE00.0290.00537.514-0.002-0.0020.0000.0000.0000.000
46A525GLU-1-0.935-0.96740.5630.0230.0230.0000.0000.0000.000
47A526ALA00.0320.01637.088-0.004-0.0040.0000.0000.0000.000
48A527ALA00.0240.00839.100-0.003-0.0030.0000.0000.0000.000
49A528ARG10.9440.96940.319-0.016-0.0160.0000.0000.0000.000
50A529ILE0-0.041-0.01740.900-0.002-0.0020.0000.0000.0000.000
51A530LEU0-0.014-0.00136.381-0.003-0.0030.0000.0000.0000.000
52A531SER0-0.078-0.02040.693-0.002-0.0020.0000.0000.0000.000
53A532VAL00.0460.00943.407-0.002-0.0020.0000.0000.0000.000
54A533PRO0-0.042-0.00545.8460.0020.0020.0000.0000.0000.000
55A534LYS10.9490.96048.704-0.012-0.0120.0000.0000.0000.000
56A535VAL00.0000.00751.943-0.001-0.0010.0000.0000.0000.000
57A536ASP-1-0.890-0.94355.3650.0030.0030.0000.0000.0000.000
58A537ASP-1-0.870-0.95057.2030.0080.0080.0000.0000.0000.000
59A538GLU-1-0.927-0.96959.9670.0060.0060.0000.0000.0000.000
60A539ILE0-0.036-0.02259.290-0.001-0.0010.0000.0000.0000.000
61A540LEU00.0060.00358.111-0.001-0.0010.0000.0000.0000.000
62A541GLY00.0240.02062.2390.0000.0000.0000.0000.0000.000
63A542PHE0-0.103-0.04965.1950.0000.0000.0000.0000.0000.000
64A543ILE0-0.054-0.01561.995-0.001-0.0010.0000.0000.0000.000
65A544SER0-0.096-0.03764.7950.0000.0000.0000.0000.0000.000
66A556SER00.023-0.01067.2590.0000.0000.0000.0000.0000.000
67A557THR0-0.028-0.01962.6490.0000.0000.0000.0000.0000.000
68A558GLU-1-0.724-0.82361.813-0.006-0.0060.0000.0000.0000.000
69A559SER00.008-0.00160.2470.0000.0000.0000.0000.0000.000
70A560CYS0-0.060-0.03158.303-0.001-0.0010.0000.0000.0000.000
71A561ASP-1-0.828-0.92857.082-0.013-0.0130.0000.0000.0000.000
72A562LYS10.8570.92456.2820.0050.0050.0000.0000.0000.000
73A563HIS10.8550.93453.3560.0140.0140.0000.0000.0000.000
74A564LEU0-0.014-0.02052.366-0.001-0.0010.0000.0000.0000.000
75A565ASP-1-0.878-0.92951.898-0.007-0.0070.0000.0000.0000.000
76A566LEU00.0280.02248.3690.0000.0000.0000.0000.0000.000
77A567ALA0-0.031-0.01847.9760.0000.0000.0000.0000.0000.000
78A568LEU00.0000.00146.936-0.002-0.0020.0000.0000.0000.000
79A569CYS00.0040.01346.7990.0000.0000.0000.0000.0000.000
80A570ARG10.8710.91443.7790.0140.0140.0000.0000.0000.000
81A571SER0-0.039-0.03742.416-0.002-0.0020.0000.0000.0000.000
82A572TYR0-0.050-0.01641.843-0.003-0.0030.0000.0000.0000.000
83A573GLU-1-0.886-0.95440.3990.0010.0010.0000.0000.0000.000
84A574ALA0-0.040-0.01838.1940.0010.0010.0000.0000.0000.000
85A575ALA00.0220.00136.866-0.001-0.0010.0000.0000.0000.000
86A576ALA00.0000.01136.9600.0000.0000.0000.0000.0000.000
87A577SER0-0.015-0.02534.6890.0040.0040.0000.0000.0000.000
88A578ALA00.0190.01532.6050.0030.0030.0000.0000.0000.000
89A579LEU0-0.0020.01132.076-0.001-0.0010.0000.0000.0000.000
90A580GLN0-0.072-0.05432.4810.0000.0000.0000.0000.0000.000
91A581ILE00.0320.01627.3590.0060.0060.0000.0000.0000.000
92A582ALA00.0190.02427.8330.0020.0020.0000.0000.0000.000
93A583ALA0-0.029-0.02128.2430.0000.0000.0000.0000.0000.000
94A584HIS0-0.032-0.03125.7970.0060.0060.0000.0000.0000.000
95A585THR0-0.007-0.01423.6630.0030.0030.0000.0000.0000.000
96A586ALA0-0.032-0.00523.720-0.002-0.0020.0000.0000.0000.000
97A587PHE0-0.032-0.01223.4480.0020.0020.0000.0000.0000.000
98A588VAL00.0570.02719.1740.0080.0080.0000.0000.0000.000
99A589ALA00.0170.01419.8880.0020.0020.0000.0000.0000.000
100A590LYS10.8800.92720.3460.0000.0000.0000.0000.0000.000
101A591SER0-0.035-0.00919.5940.0100.0100.0000.0000.0000.000
102A592LEU00.0520.03014.2580.0170.0170.0000.0000.0000.000
103A593GLN00.0220.01416.2110.0060.0060.0000.0000.0000.000
104A594ALA0-0.021-0.01618.1910.0070.0070.0000.0000.0000.000
105A595ASP-1-0.795-0.88113.9060.1880.1880.0000.0000.0000.000
106A596ILE00.001-0.00113.1910.0370.0370.0000.0000.0000.000
107A597SER0-0.037-0.01414.5650.0160.0160.0000.0000.0000.000
108A598GLN00.0130.01315.5460.0320.0320.0000.0000.0000.000
109A599ALA00.018-0.00410.7860.0430.0430.0000.0000.0000.000
110A600ALA0-0.0070.00012.8390.0600.0600.0000.0000.0000.000
111A601GLN0-0.023-0.02614.6280.0130.0130.0000.0000.0000.000
112A602ILE0-0.048-0.01112.7920.0070.0070.0000.0000.0000.000
113A603ILE0-0.014-0.0139.3530.0400.0400.0000.0000.0000.000
114A604ASN0-0.043-0.01213.137-0.035-0.0350.0000.0000.0000.000
115A605SER0-0.083-0.03616.770-0.042-0.0420.0000.0000.0000.000
116A606ASP-1-0.867-0.91917.4690.4290.4290.0000.0000.0000.000
117A607PRO00.0110.01612.9470.0770.0770.0000.0000.0000.000
118A608SER0-0.027-0.03213.3080.0810.0810.0000.0000.0000.000
119A609ASP-1-0.932-0.95312.7750.7650.7650.0000.0000.0000.000
120A610ALA0-0.012-0.0267.5670.0150.0150.0000.0000.0000.000
121A611GLN00.027-0.0037.217-0.058-0.0580.0000.0000.0000.000
122A612GLN00.0120.0249.097-0.151-0.1510.0000.0000.0000.000
123A613ALA00.0580.0219.039-0.100-0.1000.0000.0000.0000.000
124A614LEU00.014-0.0062.797-0.586-0.0980.126-0.152-0.4620.000
125A615ARG10.9190.9686.229-0.973-0.9730.0000.0000.0000.000
126A616ILE0-0.075-0.0418.914-0.131-0.1310.0000.0000.0000.000
127A617LEU00.0510.0196.340-0.078-0.0780.0000.0000.0000.000
128A618ASN00.0200.0337.002-0.197-0.1970.0000.0000.0000.000
129A619ARG10.8230.8888.037-0.245-0.2450.0000.0000.0000.000
130A620THR0-0.043-0.0269.794-0.038-0.0380.0000.0000.0000.000
131A621TYR00.0120.0138.336-0.018-0.0180.0000.0000.0000.000
132A622ASP-1-0.824-0.88110.4510.1620.1620.0000.0000.0000.000
133A623ALA00.0130.00113.135-0.013-0.0130.0000.0000.0000.000
134A624ALA0-0.033-0.02413.298-0.011-0.0110.0000.0000.0000.000
135A625SER00.012-0.00814.088-0.026-0.0260.0000.0000.0000.000
136A626TYR00.0300.01715.959-0.005-0.0050.0000.0000.0000.000
137A627LEU0-0.045-0.02317.906-0.006-0.0060.0000.0000.0000.000
138A628CYS0-0.020-0.00418.501-0.017-0.0170.0000.0000.0000.000
139A629ASP-1-0.886-0.94920.052-0.021-0.0210.0000.0000.0000.000
140A630ALA0-0.008-0.00822.2120.0010.0010.0000.0000.0000.000
141A631ALA0-0.019-0.00423.537-0.001-0.0010.0000.0000.0000.000
142A632PHE0-0.025-0.03122.406-0.005-0.0050.0000.0000.0000.000
143A633ASP-1-0.841-0.89526.549-0.006-0.0060.0000.0000.0000.000
144A634GLU-1-0.884-0.94128.180-0.037-0.0370.0000.0000.0000.000
145A635VAL0-0.042-0.01928.8960.0000.0000.0000.0000.0000.000
146A636ARG10.8180.87829.6630.0410.0410.0000.0000.0000.000
147A637MET00.0150.01332.6390.0020.0020.0000.0000.0000.000
148A638SER00.0220.00233.5590.0010.0010.0000.0000.0000.000
149A639ALA0-0.019-0.00235.2170.0000.0000.0000.0000.0000.000
150A640CYS0-0.0030.00136.4380.0030.0030.0000.0000.0000.000
151A641ALA00.0520.03138.6210.0020.0020.0000.0000.0000.000
152A642MET0-0.043-0.02338.9320.0000.0000.0000.0000.0000.000
153A643GLY00.0170.01641.2300.0000.0000.0000.0000.0000.000
154A644SER00.017-0.00242.8440.0030.0030.0000.0000.0000.000
155A645SER00.0120.01344.4930.0020.0020.0000.0000.0000.000
156A646THR0-0.061-0.04644.7780.0000.0000.0000.0000.0000.000
157A647MET00.0110.01347.1630.0010.0010.0000.0000.0000.000
158A648GLY00.0430.01348.9900.0020.0020.0000.0000.0000.000
159A649ARG10.9460.96048.3240.0420.0420.0000.0000.0000.000
160A650ARG10.7670.87847.2380.0380.0380.0000.0000.0000.000
161A651TYR00.021-0.00151.9040.0010.0010.0000.0000.0000.000
162A652LEU00.0170.00455.0140.0010.0010.0000.0000.0000.000
163A653TRP0-0.030-0.01855.2890.0000.0000.0000.0000.0000.000
164A654LEU0-0.034-0.00956.2440.0000.0000.0000.0000.0000.000
165A655LYS10.8770.92159.4200.0200.0200.0000.0000.0000.000
166A656ASP-1-0.827-0.88061.517-0.018-0.0180.0000.0000.0000.000
167A657CYS0-0.0370.02261.7000.0010.0010.0000.0000.0000.000
168A658LYS10.9660.96864.9780.0170.0170.0000.0000.0000.000
169A659ILE00.0430.01761.2810.0000.0000.0000.0000.0000.000
170A660SER00.0330.01663.2790.0010.0010.0000.0000.0000.000
171A661PRO00.0730.01061.661-0.001-0.0010.0000.0000.0000.000
172A662ALA00.0250.02859.7050.0000.0000.0000.0000.0000.000
173A663SER00.0490.01558.303-0.001-0.0010.0000.0000.0000.000
174A664LYS10.8120.89957.5700.0190.0190.0000.0000.0000.000
175A665ASN00.0250.01954.631-0.001-0.0010.0000.0000.0000.000
176A666LYS10.8750.93152.7650.0310.0310.0000.0000.0000.000
177A667LEU0-0.006-0.01352.599-0.002-0.0020.0000.0000.0000.000
178A668THR0-0.032-0.03651.961-0.002-0.0020.0000.0000.0000.000
179A669VAL00.0150.01449.347-0.001-0.0010.0000.0000.0000.000
180A670ALA0-0.0250.01447.965-0.001-0.0010.0000.0000.0000.000
181A671PRO00.0840.05143.2550.0000.0000.0000.0000.0000.000
182A672PHE0-0.059-0.01742.345-0.001-0.0010.0000.0000.0000.000
183A673LYS10.9290.95441.0960.0530.0530.0000.0000.0000.000
184A674GLY00.0800.05741.189-0.005-0.0050.0000.0000.0000.000
185A675GLY0-0.009-0.00242.5010.0000.0000.0000.0000.0000.000
186A676THR0-0.027-0.02644.8810.0030.0030.0000.0000.0000.000
187A677LEU0-0.0110.00547.4250.0000.0000.0000.0000.0000.000
188A678PHE00.0550.01249.0220.0010.0010.0000.0000.0000.000
189A679GLY0-0.0030.02647.5390.0010.0010.0000.0000.0000.000
190A680GLY0-0.014-0.02448.386-0.003-0.0030.0000.0000.0000.000
191A681GLU-1-0.845-0.89451.462-0.035-0.0350.0000.0000.0000.000
192A682VAL00.015-0.00753.0030.0020.0020.0000.0000.0000.000
193A683HIS00.0200.00555.5150.0020.0020.0000.0000.0000.000
194A684LYS10.8550.93657.1920.0390.0390.0000.0000.0000.000
195A685VAL00.0100.01159.0040.0010.0010.0000.0000.0000.000